Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| griddap | Subset | tabledap | Make A Graph | wms | files | Accessible | Title | Summary | FGDC | ISO 19115 | Info | Background Info | RSS | Institution | Dataset ID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_745527/ | public | [18S rRNA gene tag sequences from DNA and RNA] - NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series) | Raw DNA and RNA V4 tag sequences include spatially and temporally distinct samples from coastal California. Samples were collected in Niskin bottles with a CTD rosette at the San Pedro Ocean Time-series (SPOT) between April of 2013 and January of 2014. This dataset contains sequence data accession numbers and metadata for the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP070577, BioProject: PRJNA311248).\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nsample_name (unitless)\nSRA_run_ID (unitless)\nSRA_run_link (unitless)\nlibrary_ID (unitless)\nSRA_study_ID (unitless)\nSRA_title (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfiletpe2 (unitless)\nfilename2 (unitless)\ndepth2 (Depth, various)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_745527_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_745527_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_745527/index.htmlTable | https://www.bco-dmo.org/dataset/745527
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_745527.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_745527&showErrors=false&email= | BCO-DMO | bcodmo_dataset_745527 | ||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_785167.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_785167 | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_785167/ | public | [Crassostrea virginica gonad MBD-BSseq] - Eastern oyster gonad methylation patterns in response to experimental ocean acidification (Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?) | Eastern oyster gonad methylation patterns in response to experimental ocean acidification at pCO2 levels 400 and 2800 ppm. Oysters were collected from an intertidal oyster reef in Plum Island Sound, MA, Gulf of Maine in mid-July 2016. This dataset includes GenBank BioProject PRJNA513384 metadata.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfilename2 (unitless)\nMBD_cv_id (unitless)\npCO2_treatment (P CO2 Treatment, ppm)\n | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_785167_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_785167/index.htmlTable | https://www.bco-dmo.org/dataset/785167
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_785167.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_785167&showErrors=false&email= | BCO-DMO | bcodmo_dataset_785167 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_700961/ | public | [Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers] - NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) (Basin-scale genetics of marine zooplankton) | These data include sample information and accession links to sequence data at\nThe National Center for Biotechnology Information (NCBI) Sequence Read Archive\n(SRA).\n \nThis data submission consists of metabarcoding data for the zooplankton\ncommunity in the epipelagic, mesopelagic and upper bathypelagic zones\n(0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to\nassess the hidden diversity present in zooplankton assemblages in midwaters,\nand detect vertical gradients in species richness, depth distributions, and\ncommunity composition of the full zooplankton assemblage. Samples were\ncollected in June 2014 from Station ALOHA (22.75, -158) using a 1 meter square\nMultiple Opening and Closing Nets and Environmental Sampling System (MOCNESS,\n200um mesh), on R/V Falkor cruise FK140613. \\u00a0Next generation sequence\ndata (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton\nassemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers\ndescribed in Fonseca et al. 2010). The data includes sequences and read count\nabundance information for molecular OTUs from both holoplanktonic and\nmeroplanktonic taxa\n \nRelated dataset containing OTU tables and fasta sequences (representative /\nmost abundance read for each OTU): \n[Metabarcoding zooplankton at ](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[station](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[ ALOHA: OTU tables and ](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[fasta](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[ files](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)\n\ncdm_data_type = Other\nVARIABLES:\nanalysis_name (unitless)\n... (15 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_700961_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_700961_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_700961/index.htmlTable | https://www.bco-dmo.org/dataset/700961
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_700961.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_700961&showErrors=false&email= | BCO-DMO | bcodmo_dataset_700961 | ||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518 | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_745518/ | public | [Microbial eukaryotic focused metatranscriptome data] - Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015 (Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series) | Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community. Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503). Sequences for BioProject PRJNA608423 will be available at NCBI on Jan 1st, 2021.\\r\\n\\r\\nThese data were published in Hu et al. (2018).\n\ncdm_data_type = Other\nVARIABLES:\nSRA_run (unitless)\nSRA_run_link (unitless)\nSRA_study (unitless)\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nsample_name (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfilename2 (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_745518_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_745518/index.htmlTable | https://www.bco-dmo.org/dataset/745518
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_745518.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_745518&showErrors=false&email= | BCO-DMO | bcodmo_dataset_745518 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_746654/ | public | [Trichodesmium AHL metatranscriptomes_AE1409] - Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata (Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation) | Trichodesmium is a marine, diazotrophic cyanobacterium that plays a central role in the biogeochemical cycling of carbon and nitrogen. Colonies ubiquitously co-occur with a diverse microbiome of heterotrophic bacteria. Here we show that manipulation of the microbiome with quorum sensing acyl homoserine lactone (AHL) molecules significantly modulated rates of N2 fixation by Trichodesmium collected from the western North Atlantic, with both positive and negative effects of varied magnitude. Changes in Trichodesmium N2 fixation did not clearly correlate with changes in microbiome composition or geochemical patterns. Metatranscriptome sequencing revealed significant changes in the relative abundance of microbiome transcripts encoding metabolic functions consistent with quorum sensing responses in model bacteria. There was little overlap in specific microbiome transcriptional responses to AHL addition between stations, and this variability in microbiome gene expression may underpin the heterogeneous changes in Trichodesmium N2 fixation. These data suggest the microbiome could play a large and previously overlooked role in modulating Trichodesmium N2 fixation. This metadata form describes the metatranscriptomic sequencing reads that were used in the study.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nassembly (unitless)\nfilename (unitless)\n... (7 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_746654_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_746654/index.htmlTable | https://www.bco-dmo.org/dataset/746654
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_746654.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_746654&showErrors=false&email= | BCO-DMO | bcodmo_dataset_746654 |